Us Weekly -- Divorce is a tricky minefield for all kids -- including Isabella and Connor Cruise, who were just 8 and 6 years old, respectively, when their world-famous parents Tom Cruise and Nicole Kidman divorced in 2001 after 11 years together.

Maureen Orth's investigative cover story in the new Vanity Fair alleges, among other things, that members of Cruise's Church of Scientology turned the young kids against their mom, now 45, following the split.

"The central problem [in the marriage] was Nicole did not want to deal with Scientology," former high-ranking Scientologist Marty Rathbun claims to the magazine. After Kidman left the marriage and the Church, she was labeled a Suppressive Person -- a spiritually toxic person to be avoided -- with members of the Church quietly instilling this idea into the kids, sources claimed to Vanity Fair.

"They rejected Nicole -- they've been instructed," says John Brousseau, who was a Scientologist for 32 years and formerly the bodyguard and brother-in-law to church leader David Miscavige.

Bella and Connor were home schooled, and allegedly accompanied their movie star father, now 50, on auditing sessions, and were taught how to recognize an "S.P.," Rathbun and Brousseau both tell VF.

"They took a course, P.T.S./S.P., Potential Trouble Source/Suppressive Person, for persons connected in their lives who are an S.P.," Brousseau claims. "[Bella and Connor] whispered to me, 'J.B., Nicole is an S.P.! Our mom's an S.P. -- we hate going and seeing her.'"

Sources also claim in Orth's story that Kidman was so ostracized within the Scientology community that Church members were even urged to avoid her films.

"The Scientology world hated Nicole," Brousseau, who left the Church in 2010, says. "People in Sea Org were mandated to see every freaking Tom Cruise movie that came out. But if you ever mentioned an inkling to see a movie with Nicole, oh my God, you'd hear about it."

The Church of Scientology denied to Vanity Fair that Kidman was considered a Suppressive Person, or that Bella and Connor took a course on how to identify Suppressive persons.

In a later statement, the Church of Scientology roundly dismissed Orth's story, which centers around actress and former church member Nazanin Boniadi, who was allegedly audited to date Cruise and then punished by the organization for her behavior during and after the relationship. "The entire story is hogwash," the Church said.

Cruise and third wife Katie Holmes finalized their divorce last month.